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Moulistanos A, Nikolaou T, Sismanoglou S, Gkagkavouzis K, Karaiskou N, Antonopoulou E, Triantafyllidis A, Papakostas S. Investigating the role of genetic variation in vgll3 and six6 in the domestication of gilthead seabream ( Sparus aurata Linnaeus) and European seabass ( Dicentrarchus labrax Linnaeus). Ecol Evol 2023; 13:e10727. [PMID: 38020694 PMCID: PMC10654472 DOI: 10.1002/ece3.10727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Gene function conservation is crucial in molecular ecology, especially for key traits like growth and maturation in teleost fish. The vgll3 and six6 genes are known to influence age-at-maturity in Atlantic salmon, but their impact on other fish species is poorly understood. Here, we investigated the association of vgll3 and six6 in the domestication of gilthead seabream and European seabass, both undergoing selective breeding for growth-related traits in the Mediterranean. We analysed two different sets of samples using two different genotyping approaches. The first dataset comprised farmed and wild populations from Greece, genotyped for SNPs within the two genes ('gene-level genotyping'). The second dataset examined 300-600 k SNPs located in the chromosomes of the two genes, derived from a meta-analysis of a Pool-Seq experiment involving farmed and wild populations distributed widely across the Mediterranean ('chromosome-level genotyping'). The gene-level analysis revealed a statistically significant allele frequency differences between farmed and wild populations on both genes in each species. This finding was partially supported by the chromosome-level analysis, identifying highly differentiated regions may be involved in the domestication process at varying distances from the candidate genes. Noteworthy genomic features were found, such as a CpG island in gilthead seabream and novel candidate genes in European seabass, warranting further investigation. These findings support a putative role of vgll3 and six6 in the maturation and growth of gilthead seabream and European seabass, emphasizing the need for further research on their conserved function.
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Affiliation(s)
- Aristotelis Moulistanos
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Theopisti Nikolaou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
| | - Smaragda Sismanoglou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
| | - Konstantinos Gkagkavouzis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Nikoleta Karaiskou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Efthimia Antonopoulou
- Department of Zoology, School of BiologyAristotle University of ThessalonikiThessalonikiGreece
| | - Alexandros Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Spiros Papakostas
- Department of Science and TechnologyInternational Hellenic UniversityThessalonikiGreece
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Ólafsdóttir GÁ, Turnbull S, Jónsdóttir IG, Nickel A, Karlsson H, Henke T, Nielsen EE, Pálsson S. Genetic assignment predicts depth of benthic settlement for 0-group Atlantic cod. PLoS One 2023; 18:e0292495. [PMID: 37792752 PMCID: PMC10550133 DOI: 10.1371/journal.pone.0292495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Atlantic cod is a keystone species that remains among the most economically important demersal fish in the North Atlantic. Throughout its distribution range, Atlantic cod is composed of populations with varying environmental preferences and migratory propensities. This life-history variation is likely to have contributed to the niche width and large population sizes of Atlantic cod, and its relative resilience to environmental change and exploitation. The Icelandic cod stock is currently managed as a single unit, but early research indicates population variation by depth and temperature and distinct offshore and inshore spawning components. Pelagic 0-group juveniles from different spawning grounds coexist in nursery areas around Iceland, but their genetic composition or habitat partitioning had not been examined post benthic settlement. In the current study we examine the genetic composition of Atlantic cod juvenile aggregations at nearshore nursery grounds in NW-Iceland and report distinct segregation by the depth of offshore and inshore juvenile cod. The physiological mechanism of this segregation is not known, but the pattern demonstrates the need to consider population structure at nursery grounds in the application of marine spatial planning and other area-based conservation tools.
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Affiliation(s)
- Guðbjörg Ásta Ólafsdóttir
- University of Iceland, Research Centre of the Westfjords, Bolungarvík, Iceland
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
| | - Shaun Turnbull
- University of Iceland, Research Centre of the Westfjords, Bolungarvík, Iceland
| | | | - Anja Nickel
- University of Iceland, Research Centre of the Westfjords, Bolungarvík, Iceland
| | - Hjalti Karlsson
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
| | - Theresa Henke
- University of Iceland, Research Centre of the Westfjords, Bolungarvík, Iceland
| | - Einar Eg Nielsen
- DTU Aqua, National Institute of Aquatic Resources, Silkeborg, Denmark
| | - Snæbjörn Pálsson
- University of Iceland, Faculty of Life and Environmental Sciences, Reykjavík, Iceland
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Luikart G, Antao T, Hand BK, Muhlfeld CC, Boyer MC, Cosart T, Trethewey B, Al-Chockhachy R, Waples RS. Detecting population declines via monitoring the effective number of breeders (N b ). Mol Ecol Resour 2020; 21:379-393. [PMID: 32881365 DOI: 10.1111/1755-0998.13251] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022]
Abstract
Estimating the effective population size and effective number of breeders per year (Nb ) can facilitate early detection of population declines. We used computer simulations to quantify bias and precision of the one-sample LDNe estimator of Nb in age-structured populations using a range of published species life history types, sample sizes, and DNA markers. Nb estimates were biased by ~5%-10% when using SNPs or microsatellites in species ranging from fishes to mosquitoes, frogs, and seaweed. The bias (high or low) was similar for different life history types within a species suggesting that life history variation in populations will not influence Nb estimation. Precision was higher for 100 SNPs (H ≈ 0.30) than for 15 microsatellites (H ≈ 0.70). Confidence intervals (CIs) were occasionally too narrow, and biased high when Nb was small (Nb < 50); however, the magnitude of bias would unlikely influence management decisions. The CIs (from LDNe) were sufficiently narrow to achieve high statistical power (≥0.80) to reject the null hypothesis that Nb = 50 when the true Nb = 30 and when sampling 50 individuals and 200 SNPs. Similarly, CIs were sufficiently narrow to reject Nb = 500 when the true Nb = 400 and when sampling 200 individuals and 5,000 loci. Finally, we present a linear regression method that provides high power to detect a decline in Nb when sampling at least five consecutive cohorts. This study provides guidelines and tools to simulate and estimate Nb for age structured populations (https://github.com/popgengui/agestrucnb/), which should help biologists develop sensitive monitoring programmes for early detection of changes in Nb and population declines.
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Affiliation(s)
- Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Tiago Antao
- The Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Brian K Hand
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Clint C Muhlfeld
- Northern Rocky Mountain Science Center, U.S. Geological Survey, Glacier National Park, Northern Rocky Mountain Science Center, West Glacier, MT, USA
| | | | - Ted Cosart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Brian Trethewey
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Robert Al-Chockhachy
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT, USA
| | - Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
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Robledo D, Rubiolo JA, Cabaleiro S, Martínez P, Bouza C. Differential gene expression and SNP association between fast- and slow-growing turbot (Scophthalmus maximus). Sci Rep 2017; 7:12105. [PMID: 28935875 PMCID: PMC5608734 DOI: 10.1038/s41598-017-12459-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/08/2017] [Indexed: 12/20/2022] Open
Abstract
Growth is among the most important traits for animal breeding. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Here, we report a transcriptomic study in muscle and brain of fast- and slow-growing turbot (Scophthalmus maximus), a relevant flatfish in European and Asian aquaculture. Gene expression and allelic association between the two groups were explored. Up-regulation of the anaerobic glycolytic pathway in the muscle of fast-growing fish was observed, indicating a higher metabolic rate of white muscle. Brain expression differences were smaller and not associated with major growth-related genes, but with regulation of feeding-related sensory pathways. Further, SNP variants showing frequency differences between fast- and slow-growing fish pointed to genomic regions likely involved in growth regulation, and three of them were individually validated through SNP typing. Although different mechanisms appear to explain growth differences among families, general mechanisms seem also to be involved, and thus, results provide a set of useful candidate genes and markers to be evaluated for more efficient growth breeding programs and to perform comparative genomic studies of growth in fish and vertebrates.
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Affiliation(s)
- Diego Robledo
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
| | - Juan A Rubiolo
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Santiago Cabaleiro
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira, 15695, Spain
| | - Paulino Martínez
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Carmen Bouza
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain.
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Robledo D, Fernández C, Hermida M, Sciara A, Álvarez-Dios JA, Cabaleiro S, Caamaño R, Martínez P, Bouza C. Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot. Int J Mol Sci 2016; 17:243. [PMID: 26901189 PMCID: PMC4783974 DOI: 10.3390/ijms17020243] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 12/30/2022] Open
Abstract
Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species.
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Affiliation(s)
- Diego Robledo
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Carlos Fernández
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
| | - Miguel Hermida
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
| | - Andrés Sciara
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario S2002LRK, Argentina.
| | - José Antonio Álvarez-Dios
- Departamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Santiago Cabaleiro
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira 15695, Spain.
| | - Rubén Caamaño
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira 15695, Spain.
| | - Paulino Martínez
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
| | - Carmen Bouza
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
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Wenzel MA, Piertney SB. Digging for gold nuggets: uncovering novel candidate genes for variation in gastrointestinal nematode burden in a wild bird species. J Evol Biol 2015; 28:807-25. [DOI: 10.1111/jeb.12614] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/13/2015] [Accepted: 02/16/2015] [Indexed: 12/16/2022]
Affiliation(s)
- M. A. Wenzel
- Institute of Biological and Environmental Sciences; University of Aberdeen; Aberdeen UK
| | - S. B. Piertney
- Institute of Biological and Environmental Sciences; University of Aberdeen; Aberdeen UK
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Feng X, Yu X, Pang M, Liu H, Tong J. Molecular characterization and expression of three preprosomatostatin genes and their association with growth in common carp (Cyprinus carpio). Comp Biochem Physiol B Biochem Mol Biol 2014; 182:37-46. [PMID: 25536408 DOI: 10.1016/j.cbpb.2014.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 12/21/2022]
Abstract
Somatostatins (SSs) are a structurally diverse family of peptides that play important roles in the regulation of growth, development and metabolism in vertebrates. In this study, three preprosomatostatin genes (PSSs) in the common carp, Cyprinus carpio (Cc) were identified and characterized. Based on cloned sequences and genome BLAST, six isoforms of the PSS gene in C. carpio (CcPSS) were identified and included CcPSS1a and CcPSS1b, CcPSS2a and CcPSS2b, and finally, CcPSS3a and CcPSS3b. The open reading frames (ORF) of CcPSS1a, CcPSS2a and CcPSS3a consist of 345, 336 and 363 nucleotides. During embryonic development, the expressions of CcPSS2 and CcPSS3 were first observed at the stage of optic vesicle, and CcPSS1 mRNA was initially detected at the stage of muscular effect. The highest mRNA levels of CcPSS1, CcPSS2 and CcPSS3 were observed at 1-day post-hatch (dph), 2-dph and the stage of heart beating, respectively. In the adult brain, the distributions of three CcPSS mRNAs were differential but overlapping in the hypothalamus, telencephalon and medulla oblongata. For peripheral tissues, all three CcPSS mRNAs were detected in the mid-intestine, and CcPSS1 and CcPSS3 mRNAs were also expressed in the liver. Owing to the importance of somatostatins on regulating growth, functional mutations of CcPSSs were identified in a C. carpio population. A total of 23 polymorphic sites were detected in CcPSS1a and CcPSS3a. Of them, two SNPs (CcPSS1a-g.922C>T, and CcPSS3a-g.1125C>A) were significantly associated with growth traits, indicating their potential applications in gene (marker)-assisted selective breeding in C. carpio.
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Affiliation(s)
- Xiu Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China
| | - Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
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Qi J, Liu X, Liu J, Yu H, Wang W, Wang Z, Zhang Q. Molecular characterization of heat shock protein 70 (HSP 70) promoter in Japanese flounder (Paralichthys olivaceus), and the association of Pohsp70 SNPs with heat-resistant trait. FISH & SHELLFISH IMMUNOLOGY 2014; 39:503-511. [PMID: 24925759 DOI: 10.1016/j.fsi.2014.05.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 06/03/2023]
Abstract
Ambient temperature is one of the major abiotic environmental factors determining the main parameters of fish vital activity. HSP70 plays an essential role in heat response. In this investigation, the promoter and structure of Paralichthys olivaceus hsp70 (Pohsp70) gene was cloned and predicted. 2558 bp upstream regulatory region of Pohsp70 was annotated with four potential promoter elements and four putative binding sites of transcription factors heat shock elements (HSE, nGAAn) in the upstream of the transcription start site. In addition, one intron with 454 bp in the 5'-noncoding region was found. Quantitative Real Time PCR analysis indicated that the transcript level of Pohsp70 was raised markedly after 1 h by heat shocked. Furthermore, 25 SNPs were identified in Pohsp70 by resequencing, seven of which was associated with heat resistance. In addition, two of the seven SNPs, namely SNP14 and SNP16, were observed in strong linkage disequilibrium. The haplotype with association analysis showed TAGGAG haplotype was more represented in heat susceptible group while (DEL/T) GAATA haplotype was more frequent in heat resistant group. The heat resistant SNPs and haplotype could be candidate markers potentially serving for selective breeding programs of Japanese flounder aimed at improving anti-stress and production.
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Affiliation(s)
- Jie Qi
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 266003 Qingdao, Shandong, China
| | - Xudong Liu
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 266003 Qingdao, Shandong, China
| | - Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 266003 Qingdao, Shandong, China
| | - Haiyang Yu
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 266003 Qingdao, Shandong, China
| | - Wenji Wang
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 266003 Qingdao, Shandong, China
| | - Zhigang Wang
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 266003 Qingdao, Shandong, China
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 266003 Qingdao, Shandong, China.
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Allendorf FW, Berry O, Ryman N. So long to genetic diversity, and thanks for all the fish. Mol Ecol 2014; 23:23-5. [PMID: 24372752 DOI: 10.1111/mec.12574] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 10/17/2013] [Accepted: 10/23/2013] [Indexed: 11/30/2022]
Abstract
The world faces a global fishing crisis. Wild marine fisheries comprise nearly 15% of all animal protein in the human diet, but, according to the U.N. Food and Agriculture Organization, nearly 60% of all commercially important marine fish stocks are overexploited, recovering, or depleted (FAO 2012; Fig. 1). Some authors have suggested that the large population sizes of harvested marine fish make even collapsed populations resistant to the loss of genetic variation by genetic drift (e.g. Beverton 1990). In contrast, others have argued that the loss of alleles because of overfishing may actually be more dramatic in large populations than in small ones (Ryman et al. 1995). In this issue, Pinsky & Palumbi (2014) report that overfished populations have approximately 2% lower heterozygosity and 12% lower allelic richness than populations that are not overfished. They also performed simulations which suggest that their estimates likely underestimate the actual loss of rare alleles by a factor of three or four. This important paper shows that the harvesting of marine fish can have genetic effects that threaten the long-term sustainability of this valuable resource.
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Affiliation(s)
- Fred W Allendorf
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA; Walpole Marine Fish Genetics Group, North Walpole Road, Walpole, WA, 6398, Australia
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10
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Proestou DA, Flight P, Champlin D, Nacci D. Targeted approach to identify genetic loci associated with evolved dioxin tolerance in Atlantic killifish (Fundulus heteroclitus). BMC Evol Biol 2014; 14:7. [PMID: 24422627 PMCID: PMC4029433 DOI: 10.1186/1471-2148-14-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 12/30/2013] [Indexed: 11/10/2022] Open
Abstract
Background The most toxic aromatic hydrocarbon pollutants are categorized as dioxin-like compounds (DLCs) to which extreme tolerance has evolved independently and contemporaneously in (at least) four populations of Atlantic killifish (Fundulus heteroclitus). Surprisingly, the magnitude and phenotype of DLC tolerance is similar among these killifish populations that have adapted to varied, but highly aromatic hydrocarbon-contaminated urban/industrialized estuaries of the US Atlantic coast. Multiple tolerant and neighboring sensitive killifish populations were compared with the expectation that genetic loci associated with DLC tolerance would be revealed. Results Since the aryl hydrocarbon receptor (AHR) pathway partly or fully mediates DLC toxicity in vertebrates, single nucleotide polymorphisms (SNPs) from 42 genes associated with the AHR pathway were identified to serve as targeted markers. Wild fish (N = 36/37) from four highly tolerant killifish populations and four nearby sensitive populations were genotyped using 59 SNP markers. Similar to other killifish population genetic analyses, strong genetic differentiation among populations was detected, consistent with isolation by distance models. When DLC-sensitive populations were pooled and compared to pooled DLC-tolerant populations, multi-locus analyses did not distinguish the two groups. However, pairwise comparisons of nearby tolerant and sensitive populations revealed high differentiation among sensitive and tolerant populations at these specific loci: AHR 1 and 2, cathepsin Z, the cytochrome P450s (CYP1A and 3A30), and the NADH dehydrogenase subunits. In addition, significant shifts in minor allele frequency were observed at AHR2 and CYP1A loci across most sensitive/tolerant pairs, but only AHR2 exhibited shifts in the same direction across all pairs. Conclusions The observed differences in allelic composition at the AHR2 and CYP1A SNP loci were identified as significant among paired sensitive/tolerant populations of Atlantic killifish with multiple statistical tests. The genetic patterns reported here lend support to the argument that AHR2 and CYP1A play a role in the adaptive response to extreme DLC contamination. Additional functional assays are required to isolate the exact mechanism of DLC tolerance.
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Affiliation(s)
- Dina A Proestou
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, 27 Tarzwell Drive, Narragansett, RI 02882, USA.
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11
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Milano I, Babbucci M, Cariani A, Atanassova M, Bekkevold D, Carvalho GR, Espiñeira M, Fiorentino F, Garofalo G, Geffen AJ, Hansen JH, Helyar SJ, Nielsen EE, Ogden R, Patarnello T, Stagioni M, Tinti F, Bargelloni L. Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius). Mol Ecol 2013; 23:118-35. [DOI: 10.1111/mec.12568] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 01/27/2023]
Affiliation(s)
- Ilaria Milano
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science-Agripolis-Viale dell'Università 16; I-35020 Legnaro Padova Italy
| | - Alessia Cariani
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Miroslava Atanassova
- Living Resources, Aquaculture and Management of their Traceability Division of ANFACO-CECOPESCA; Ctra. Colegio Universitario 16; 36.310 Vigo Spain
| | - Dorte Bekkevold
- National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 DK-8600 Silkeborg Denmark
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory; School of Biological Sciences; Bangor University; Environment Centre Wales; Bangor UK
| | - Montserrat Espiñeira
- Living Resources, Aquaculture and Management of their Traceability Division of ANFACO-CECOPESCA; Ctra. Colegio Universitario 16; 36.310 Vigo Spain
| | - Fabio Fiorentino
- National Research Council (CNR)-Institute for Coastal Marine Environment (IAMC); Via L. Vaccara 61 91026 Mazara del Vallo Trapani Italy
| | - Germana Garofalo
- National Research Council (CNR)-Institute for Coastal Marine Environment (IAMC); Via L. Vaccara 61 91026 Mazara del Vallo Trapani Italy
| | - Audrey J. Geffen
- Department of Biology; University of Bergen; P.O. Box 7803, N-5020 Bergen Norway
| | - Jakob. H. Hansen
- Living Resources, Aquaculture and Management of their Traceability Division of ANFACO-CECOPESCA; Ctra. Colegio Universitario 16; 36.310 Vigo Spain
| | - Sarah J. Helyar
- Food Safety, Environment & Genetics; Matís ohf, Vínlandsleið 12; 113 Reykjavík Iceland
| | - Einar E. Nielsen
- National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 DK-8600 Silkeborg Denmark
| | - Rob Ogden
- TRACE Wildlife Forensics Network; Royal Zoological Society of Scotland; Edinburgh EH12 6TS UK
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science-Agripolis-Viale dell'Università 16; I-35020 Legnaro Padova Italy
| | - Marco Stagioni
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Fausto Tinti
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science-Agripolis-Viale dell'Università 16; I-35020 Legnaro Padova Italy
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12
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Conserving marine biodiversity: insights from life-history trait candidate genes in Atlantic cod (Gadus morhua). CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0532-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Ross SD, Behrens JW, Brander K, Methling C, Mork J. Haemoglobin genotypes in cod (Gadus morhua L): Their geographic distribution and physiological significance. Comp Biochem Physiol A Mol Integr Physiol 2013; 166:158-68. [DOI: 10.1016/j.cbpa.2013.05.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/21/2013] [Accepted: 05/24/2013] [Indexed: 11/26/2022]
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14
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Niu D, Wang L, Sun F, Liu Z, Li J. Development of molecular resources for an intertidal clam, Sinonovacula constricta, using 454 transcriptome sequencing. PLoS One 2013; 8:e67456. [PMID: 23935831 PMCID: PMC3723811 DOI: 10.1371/journal.pone.0067456] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/17/2013] [Indexed: 12/02/2022] Open
Abstract
Background The razor clam Sinonovacula constricta is a benthic intertidal bivalve species with important commercial value. Despite its economic importance, knowledge of its transcriptome is scarce. Next generation sequencing technologies offer rapid and efficient tools for generating large numbers of sequences, which can be used to characterize the transcriptome, to develop effective molecular markers and to identify genes associated with growth, a key breeding trait. Results Total RNA was isolated from the mantle, gill, liver, siphon, gonad and muscular foot tissues. High-throughput deep sequencing of S. constricta using 454 pyrosequencing technology yielded 859,313 high-quality reads with an average read length of 489 bp. Clustering and assembly of these reads produced 16,323 contigs and 131,346 singletons with average lengths of 1,376 bp and 458 bp, respectively. Based on transcriptome sequencing, 14,615 sequences had significant matches with known genes encoding 147,669 predicted proteins. Subsequently, previously unknown growth-related genes were identified. A total of 13,563 microsatellites (SSRs) and 13,634 high-confidence single nucleotide polymorphism loci (SNPs) were discovered, of which almost half were validated. Conclusion De novo sequencing of the razor clam S. constricta transcriptome on the 454 GS FLX platform generated a large number of ESTs. Candidate growth factors and a large number of SSRs and SNPs were identified. These results will impact genetic studies of S. constricta.
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Affiliation(s)
- Donghong Niu
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, China
| | - Lie Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, China
| | - Fanyue Sun
- Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, United States of America
| | - Zhanjiang Liu
- Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, United States of America
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, China
- * E-mail:
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15
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Therkildsen NO, Hemmer-Hansen J, Als TD, Swain DP, Morgan MJ, Trippel EA, Palumbi SR, Meldrup D, Nielsen EE. Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod. Mol Ecol 2013; 22:2424-40. [PMID: 23551301 DOI: 10.1111/mec.12260] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 12/29/2012] [Accepted: 01/09/2013] [Indexed: 01/09/2023]
Abstract
Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an effect of directional selection, in either time, space or both. Exploratory analysis suggested that temporal allele frequency shifts at certain loci may correlate with local temperature variation and with life history changes suggested to be fisheries induced. Interestingly, however, largely nonoverlapping sets of loci were temporal outliers in the different populations and outliers from the 1928 to 1960 period showed almost complete stability during later decades. The contrasting microevolutionary trajectories among populations resulted in sequential shifts in spatial outliers, with no locus maintaining elevated spatial differentiation throughout the study period. Simulations of migration coupled with observations of temporally stable spatial structure at neutral loci suggest that population replacement or gene flow alone could not explain all the observed allele frequency variation. Thus, the genetic changes are likely to at least partly be driven by highly dynamic temporally and spatially varying selection. These findings have important implications for our understanding of local adaptation and evolutionary potential in high gene flow organisms and underscore the need to carefully consider all dimensions of biocomplexity for evolutionarily sustainable management.
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Affiliation(s)
- Nina O Therkildsen
- Section for Population Ecology and Genetics, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark.
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16
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Therkildsen NO, Hemmer-Hansen J, Hedeholm RB, Wisz MS, Pampoulie C, Meldrup D, Bonanomi S, Retzel A, Olsen SM, Nielsen EE. Spatiotemporal SNP analysis reveals pronounced biocomplexity at the northern range margin of Atlantic cod Gadus morhua. Evol Appl 2013; 6:690-705. [PMID: 23789034 PMCID: PMC3684748 DOI: 10.1111/eva.12055] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/23/2012] [Accepted: 01/03/2013] [Indexed: 12/18/2022] Open
Abstract
Accurate prediction of species distribution shifts in the face of climate change requires a sound understanding of population diversity and local adaptations. Previous modeling has suggested that global warming will lead to increased abundance of Atlantic cod (Gadus morhua) in the ocean around Greenland, but the dynamics of earlier abundance fluctuations are not well understood. We applied a retrospective spatiotemporal population genomics approach to examine the temporal stability of cod population structure in this region and to search for signatures of divergent selection over a 78-year period spanning major demographic changes. Analyzing >900 gene-associated single nucleotide polymorphisms in 847 individuals, we identified four genetically distinct groups that exhibited varying spatial distributions with considerable overlap and mixture. The genetic composition had remained stable over decades at some spawning grounds, whereas complete population replacement was evident at others. Observations of elevated differentiation in certain genomic regions are consistent with adaptive divergence between the groups, indicating that they may respond differently to environmental variation. Significantly increased temporal changes at a subset of loci also suggest that adaptation may be ongoing. These findings illustrate the power of spatiotemporal population genomics for revealing biocomplexity in both space and time and for informing future fisheries management and conservation efforts.
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Affiliation(s)
- Nina Overgaard Therkildsen
- Section for Population Ecology and -Genetics, National Institute of Aquatic Resources, Technical University of Denmark Silkeborg, Denmark ; Greenland Climate Research Centre, Greenland Institute of Natural Resources Nuuk, Greenland
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17
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Carlsson J, Gauthier DT, Carlsson JEL, Coughlan JP, Dillane E, Fitzgerald RD, Keating U, McGinnity P, Mirimin L, Cross TF. Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua. JOURNAL OF FISH BIOLOGY 2013; 82:944-958. [PMID: 23464553 DOI: 10.1111/jfb.12034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 11/21/2012] [Indexed: 06/01/2023]
Abstract
By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.
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Affiliation(s)
- J Carlsson
- Beaufort Genetics Research Programme, School of Biological, Earth and Environmental Sciences/Aquauculture and Fisheries Development Centre, University College Cork, Distillery Fields, North Mall, Cork, Ireland.
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18
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Diopere E, Hellemans B, Volckaert FA, Maes GE. Identification and validation of single nucleotide polymorphisms in growth- and maturation-related candidate genes in sole (Solea solea L.). Mar Genomics 2013; 9:33-8. [DOI: 10.1016/j.margen.2012.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/27/2012] [Accepted: 09/28/2012] [Indexed: 11/29/2022]
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19
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Genotyping of two populations of Southern Baltic Sea trout Salmo trutta m. trutta using an Atlantic salmon derived SNP-array. Mar Genomics 2013; 9:25-32. [DOI: 10.1016/j.margen.2012.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 08/23/2012] [Accepted: 08/30/2012] [Indexed: 11/20/2022]
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20
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Hoffman JI, Tucker R, Bridgett SJ, Clark MS, Forcada J, Slate J. Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal. Mol Ecol Resour 2012; 12:861-72. [PMID: 22727236 DOI: 10.1111/j.1755-0998.2012.03158.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although single nucleotide polymorphisms (SNPs) are increasingly being recognized as powerful molecular markers, their application to non-model organisms can bring significant challenges. Among these are imperfect conversion rates of assays designed from in silico resources and the enhanced potential for genotyping error relative to pre-validated, highly optimized human SNPs. To explore these issues, we used Illumina's GoldenGate assay to genotype 480 Antarctic fur seal (Arctocephalus gazella) individuals at 144 putative SNPs derived from a 454 transcriptome assembly. One hundred and thirty-five polymorphic SNPs (93.8%) were automatically validated by the program GenomeStudio, and the initial genotyping error rate, estimated from nine replicate samples, was 0.004 per reaction. However, an almost tenfold further reduction in the error rate was achieved by excluding 31 loci (21.5%) that exhibited unclear clustering patterns, manually editing clusters to allow rescoring of ambiguous or incorrect genotypes, and excluding 18 samples (3.8%) with unreliable genotypes. After stringent quality filtering, we also found a counter-intuitive negative relationship between in silico minor allele frequency and the conversion rate, suggesting that some of our assays may have been designed from paralogous loci. Nevertheless, we obtained over 45 000 individual SNP genotypes with a final error rate of 0.0005, indicating that the GoldenGate assay is eminently capable of generating large, high-quality data sets for non-model organisms. This has positive implications for future studies of the evolutionary, behavioural and conservation genetics of natural populations.
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Affiliation(s)
- J I Hoffman
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany.
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21
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Nielsen EE, Cariani A, Aoidh EM, Maes GE, Milano I, Ogden R, Taylor M, Hemmer-Hansen J, Babbucci M, Bargelloni L, Bekkevold D, Diopere E, Grenfell L, Helyar S, Limborg MT, Martinsohn JT, McEwing R, Panitz F, Patarnello T, Tinti F, Van Houdt JKJ, Volckaert FAM, Waples RS, Carvalho GR. Gene-associated markers provide tools for tackling illegal fishing and false eco-certification. Nat Commun 2012; 3:851. [DOI: 10.1038/ncomms1845] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 04/12/2012] [Indexed: 11/09/2022] Open
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22
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Hansen MM, Olivieri I, Waller DM, Nielsen EE. Monitoring adaptive genetic responses to environmental change. Mol Ecol 2012; 21:1311-29. [PMID: 22269082 DOI: 10.1111/j.1365-294x.2011.05463.x] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Widespread environmental changes including climate change, selective harvesting and landscape alterations now greatly affect selection regimes for most organisms. How animals and plants can adapt to these altered environments via contemporary evolution is thus of strong interest. We discuss how to use genetic monitoring to study adaptive responses via repeated analysis of the same populations over time, distinguishing between phenotypic and molecular genetics approaches. After describing monitoring designs, we develop explicit criteria for demonstrating adaptive responses, which include testing for selection and establishing clear links between genetic and environmental change. We then review a few exemplary studies that explore adaptive responses to climate change in Drosophila, selective responses to hunting and fishing, and contemporary evolution in Daphnia using resurrected resting eggs. We further review a broader set of 44 studies to assess how well they meet the proposed criteria, and conclude that only 23% fulfill all criteria. Approximately half (43%) of these studies failed to rule out the alternative hypothesis of replacement by a different, better-adapted population. Likewise, 34% of the studies based on phenotypic variation did not test for selection as opposed to drift. These shortcomings can be addressed via improved experimental designs and statistical testing. We foresee monitoring of adaptive responses as a future valuable tool in conservation biology, for identifying populations unable to evolve at sufficiently high rates and for identifying possible donor populations for genetic rescue. Technological advances will further augment the realization of this potential, especially next-generation sequencing technologies that allow for monitoring at the level of whole genomes.
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Affiliation(s)
- Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C, Denmark.
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23
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Zelenina DA, Martinsohn JT, Ogden R, Volkov AA, Zelenina IA, Carvalho GR. Advanced approaches to studying the population diversity of marine fishes: New opportunities for fisheries control and management. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411120179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake. PLoS One 2011; 6:e28008. [PMID: 22132191 PMCID: PMC3222667 DOI: 10.1371/journal.pone.0028008] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 10/29/2011] [Indexed: 11/19/2022] Open
Abstract
The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).
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25
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26
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Seeb JE, Carvalho G, Hauser L, Naish K, Roberts S, Seeb LW. Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Mol Ecol Resour 2011; 11 Suppl 1:1-8. [PMID: 21429158 DOI: 10.1111/j.1755-0998.2010.02979.x] [Citation(s) in RCA: 232] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- J E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, 98195, USA.
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27
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HELYAR SJ, HEMMER-HANSEN J, BEKKEVOLD D, TAYLOR MI, OGDEN R, LIMBORG MT, CARIANI A, MAES GE, DIOPERE E, CARVALHO GR, NIELSEN EE. Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Mol Ecol Resour 2011; 11 Suppl 1:123-36. [DOI: 10.1111/j.1755-0998.2010.02943.x] [Citation(s) in RCA: 315] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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28
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Seeb JE, Pascal CE, Grau ED, Seeb LW, Templin WD, Harkins T, Roberts SB. Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids. Mol Ecol Resour 2010; 11:335-48. [PMID: 21429141 DOI: 10.1111/j.1755-0998.2010.02936.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Until recently, single nucleotide polymorphism (SNP) discovery in nonmodel organisms faced many challenges, often depending upon a targeted-gene approach and Sanger sequencing of many individuals. The advent of next-generation sequencing technologies has dramatically improved discovery, but validating and testing SNPs for use in population studies remain labour intensive. Here, we detail a SNP discovery and validation pipeline that incorporates 454 pyrosequencing, high-resolution melt analysis (HRMA) and 5' nuclease genotyping. We generated 4.59×10(8) bp of redundant sequence from transcriptomes of two individual chum salmon, a highly valued species across the Pacific Rim. Nearly 26000 putative SNPs were identified--some as heterozygotes and some as homozygous for different nucleotides in the two individuals. For validation, we selected 202 templates containing single putative SNPs and conducted HRMA on 10 individuals from each of 19 populations from across the species range. Finally, 5' nuclease genotyping validated 37 SNPs that conformed to Hardy-Weinberg equilibrium expectations. Putative SNPs expressed as heterozygotes in an ascertainment individual had more than twice the validation rate of those homozygous for different alleles in the two fish, suggesting that many of the latter may have been paralogous sequence variants. Overall, this validation rate of 37/202 suggests that we have found more than 4500 templates containing SNPs for use in this population set. We anticipate using this pipeline to significantly expand the number of SNPs available for the studies of population structure and mixture analyses as well as for the studies of adaptive genetic variation in nonmodel organisms.
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Affiliation(s)
- J E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195-5020, USA
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